diff options
Diffstat (limited to 'science')
| -rw-r--r-- | science/Makefile | 1 | ||||
| -rw-r--r-- | science/libghemical/Makefile | 36 | ||||
| -rw-r--r-- | science/libghemical/distinfo | 3 | ||||
| -rw-r--r-- | science/libghemical/files/ghemical-f2c.sh | 16 | ||||
| -rw-r--r-- | science/libghemical/files/patch-configure.ac | 48 | ||||
| -rw-r--r-- | science/libghemical/pkg-descr | 3 | ||||
| -rw-r--r-- | science/libghemical/pkg-plist | 75 |
7 files changed, 182 insertions, 0 deletions
diff --git a/science/Makefile b/science/Makefile index cc1f375..10d099d 100644 --- a/science/Makefile +++ b/science/Makefile @@ -50,6 +50,7 @@ SUBDIR += kst SUBDIR += lamprop SUBDIR += libctl + SUBDIR += libghemical SUBDIR += libsvm SUBDIR += libsvm-python SUBDIR += mayavi diff --git a/science/libghemical/Makefile b/science/libghemical/Makefile new file mode 100644 index 0000000..65ff217 --- /dev/null +++ b/science/libghemical/Makefile @@ -0,0 +1,36 @@ +# New ports collection makefile for: libghemical +# Date created: July 3, 2006 +# Whom: Nakata Maho <maho@FreeBSD.org> +# +# $FreeBSD$ + +PORTNAME= libghemical +PORTVERSION= 2.00 +CATEGORIES= science +MASTER_SITES= http://www.uku.fi/~thassine/projects/download/ \ + http://bioinformatics.org/ghemical/download/ +DISTNAME= ${PORTNAME}-${PORTVERSION} + +MAINTAINER= maho@FreeBSD.org +COMMENT= Support libraries of science/ghemical port + +BUILD_DEPENDS= ${LOCALBASE}/lib/libmpqc.a:${PORTSDIR}/science/mpqc \ + openbabel:${PORTSDIR}/science/openbabel \ + mopac7:${PORTSDIR}/biology/mopac + +USE_GMAKE= yes +USE_GNOME= pkgconfig +GNU_CONFIGURE= yes +CONFIGURE_ARGS= --enable-mopac7 --enable-mpqc --enable-openbabel \ + --with-blas="-L${LOCALBASE}/lib -lf77blas -lcblas -latlas" \ + --with-lapack=-lalapack + +USE_AUTOTOOLS= autoconf:259 +PLIST_SUB= LIBGHEMICAL_VERSION="${PORTVERSION}" + +.include <bsd.port.pre.mk> + +pre-configure: + @cd ${WRKDIR}/${DISTNAME} ; ${AUTOCONF} + +.include <bsd.port.post.mk> diff --git a/science/libghemical/distinfo b/science/libghemical/distinfo new file mode 100644 index 0000000..5e9297d --- /dev/null +++ b/science/libghemical/distinfo @@ -0,0 +1,3 @@ +MD5 (libghemical-2.00.tar.gz) = 19ee087b6f3c0ce816ed1722b4a5b002 +SHA256 (libghemical-2.00.tar.gz) = e873b3042df75fa1c9f37fc99f2ff14227965ed13c7680169f714ab6575d5f21 +SIZE (libghemical-2.00.tar.gz) = 629479 diff --git a/science/libghemical/files/ghemical-f2c.sh b/science/libghemical/files/ghemical-f2c.sh new file mode 100644 index 0000000..9a1a372 --- /dev/null +++ b/science/libghemical/files/ghemical-f2c.sh @@ -0,0 +1,16 @@ +# +# Make new c sources from fortran sources, restore changes, +# made by Tommi Hassinen (3 comments are corrected additionally). +# Should be started in miniMOPAC directory. + +f2c fortran/*.f +cp fortran/*.c ./ +sed -e 's,/\* fortran/\(.*\)\.f -- translated by f2c (version 20000817),/\* \1.f -- translated by f2c (version 19991025),' \ +-e 's,dscal_,mMdscal_,g' \ +-e 's,dswap_,mMdswap_,g' \ +-e 's,daxpy_,mMdaxpy_,g' \ +-i '' *.c +mv etime.c etime.c.orig +head -18 etime.c.orig > etime.c +echo '#include <time.h>' >> etime.c +tail +19 etime.c.orig >> etime.c diff --git a/science/libghemical/files/patch-configure.ac b/science/libghemical/files/patch-configure.ac new file mode 100644 index 0000000..9487ccf --- /dev/null +++ b/science/libghemical/files/patch-configure.ac @@ -0,0 +1,48 @@ +--- configure.ac.orig Mon Apr 24 19:58:14 2006 ++++ configure.ac Mon Jul 3 10:54:47 2006 +@@ -46,6 +46,16 @@ + ;; + esac + ++AC_ARG_WITH(blas, ++[ --with-blas Gives BLAS name you use(e.g., -lblas).], ++BLAS=$withval ++) ++ ++AC_ARG_WITH(lapack, ++[ --with-lapack Gives LAPACK name you use(e.g., -llapack).], ++LAPACK=$withval ++) ++ + AC_ARG_ENABLE(mpqc,[ --enable-mpqc compile with MPQC support],WITH_MPQC="$enableval",WITH_MPQC="no") + AC_ARG_ENABLE(mopac7,[ --enable-mopac7 compile with MOPAC7 support],WITH_MOPAC7="$enableval",WITH_MOPAC7="no") + ##removed20060208##AC_ARG_ENABLE(openbabel,[ --enable-openbabel compile with OpenBabel support],WITH_OPENBABEL="$enableval",WITH_OPENBABEL="no") +@@ -69,8 +79,26 @@ + AC_CHECK_LIB([m], [acos]) + + if test $WITH_MPQC = yes; then +- AC_CHECK_LIB([blas], [main], , AC_MSG_ERROR([Cannot find blas library needed for MPQC support])) +- AC_CHECK_LIB([lapack], [main], , AC_MSG_ERROR([Cannot find lapack library needed for MPQC support])) ++ ++#Blas and lapack ...actually not checked... ++BLAS="" ++ if test "$BLASNAME" = NONE; then ++ AC_MSG_ERROR([BLAS is required to complete the build]) ++ else ++ HAVE_BLAS="yes" ++ BLAS="$BLASNAME" ++ fi ++ ++ AC_SUBST(HAVE_BLAS) ++ ++LAPACK="" ++if test "$LAPACKNAME" = NONE; then ++ AC_MSG_ERROR([LAPACK is required to complete the build]) ++else ++ HAVE_LAPACK="yes" ++ LAPACK="$LAPACKNAME" ++fi ++ + AM_PATH_SC(1.2.5, HAVE_MPQC="yes", HAVE_MPQC="no") + if test "${HAVE_MPQC}" = "yes"; then + AC_DEFINE([ENABLE_MPQC], [], [Define if you are building a version that interfaces directly with MPQC]) diff --git a/science/libghemical/pkg-descr b/science/libghemical/pkg-descr new file mode 100644 index 0000000..a804fdc --- /dev/null +++ b/science/libghemical/pkg-descr @@ -0,0 +1,3 @@ +libghemical is a support library packages for biology/ghemical + +WWW: http://www.uku.fi/~thassine/projects/ghemical/ diff --git a/science/libghemical/pkg-plist b/science/libghemical/pkg-plist new file mode 100644 index 0000000..99a3ff4 --- /dev/null +++ b/science/libghemical/pkg-plist @@ -0,0 +1,75 @@ +include/ghemical/libghemicaldefine.h +include/ghemical/libghemicalconfig2.h +include/ghemical/typedef.h +include/ghemical/v3d.h +include/ghemical/atom.h +include/ghemical/bond.h +include/ghemical/constraint.h +include/ghemical/model.h +include/ghemical/engine.h +include/ghemical/typerule.h +include/ghemical/utility.h +include/ghemical/seqbuild.h +include/ghemical/eng1_qm.h +include/ghemical/eng1_qm_mpqc.h +include/ghemical/eng1_qm_mopac.h +include/ghemical/eng1_mm.h +include/ghemical/eng1_mm_tripos52.h +include/ghemical/tab_mm_tripos52.h +include/ghemical/eng1_mm_default.h +include/ghemical/tab_mm_default.h +include/ghemical/eng1_mm_prmfit.h +include/ghemical/tab_mm_prmfit.h +include/ghemical/eng1_sf.h +include/ghemical/eng1_sf_ua.h +include/ghemical/eng1_sf_cg.h +include/ghemical/eng2_qm_mm.h +include/ghemical/notice.h +include/ghemical/conjgrad.h +include/ghemical/intcrd.h +include/ghemical/search.h +include/ghemical/geomopt.h +include/ghemical/moldyn.h +include/ghemical/pop_ana.h +include/ghemical/resonance.h +@dirrm include/ghemical +lib/libghemical.so.0 +lib/libghemical.la +lib/libghemical.a +lib/pkgconfig/libghemical.pc +share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_amino02.in +share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_aminoct02.in +share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_aminont02.in +share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_nuc02.in +share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/parm99.dat +share/libghemical/%%LIBGHEMICAL_VERSION%%/builder/amino.txt +share/libghemical/%%LIBGHEMICAL_VERSION%%/builder/nucleic.txt +share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/default/atomtypes.txt +share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/default/parameters1.txt +share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/default/parameters2.txt +share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/default/parameters3.txt +share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/default/parameters4.txt +share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/prmfit/atomtypes.txt +share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/prmfit/parameters1.txt +share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/prmfit/parameters2.txt +share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/prmfit/parameters3.txt +share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/prmfit/parameters4.txt +share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/tripos52/atomtypes.txt +share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/tripos52/parameters1.txt +share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/tripos52/parameters2.txt +share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/tripos52/parameters3.txt +share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/tripos52/parameters4.txt +share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/tripos52/parameters5.txt +share/libghemical/%%LIBGHEMICAL_VERSION%%/param_sf/default/loopdip.txt +share/libghemical/%%LIBGHEMICAL_VERSION%%/param_sf/default/looptor.txt +share/libghemical/%%LIBGHEMICAL_VERSION%%/param_sf/default/nonbonded.txt +@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_sf/default +@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_sf +@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/tripos52 +@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/prmfit +@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/default +@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm +@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/amber +@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/builder +@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%% +@dirrm share/libghemical |
